Please post a URL to your site so we can look for you. Without a link to page where the problem is on your site it is quite hard for us to provide the best solution due to so many variables. We try to provide file names and line numbers for code changes and if changes have already been made then our advice may be incorrect.
When we release upgrades template files will change and you will have to reapply all your changes again (that's if you can remember where they all are). If you keep your changes in a separate Custom CSS file you'll have no issues upgrading.